Nav-Mesh in low areas

I’m having a bit of trouble figuring out how to do my navigation inside low areas (specifically ventilations). I have small creatures sliming their way through the ventilations with a little neat climbing system that works great and so on. The navigation works fine if I place and scale the nav-meshes neatly onto the surfaces which should be navigatable. However If I encompass the entire mesh (ventilation duct in this case) with the nav-mesh it seems to default towards targeting the highest collidable area. This seems true unless there’s a significant height differences between the areas (about 280 cm) changing the navigation mesh settings agent height and adding small agents seem to have no impact.

In the first image you can see the nav mesh scaled down just to cover the bottom (which should be navigatable), the white rectangles are simply the engine cube scaled.

In the second image you can see the nav mesh encompass all meshes, the height difference between the left-most rectangles are 280 cm (center distance with a height of 10cm)

Normally I would just place a lot of neatly placed navigation volumes and no problems, however this specific project are for procedurally generated levels, hence I have to use a huge navigation volume encompassing the whole potential map.

Thanks in advance!

Any luck on this?